#load("counts_raw_and_log_180112.rda")
#load("counts_ercc.rda")
#this is better because it will work for anyone that has your package installed
#and therefore is more reproduciable.
load(system.file('rawData/counts_raw_and_log_180112.rda', package = "sp.scRNAseqAnalysis"))
load(system.file('rawData/counts_ercc.rda', package = "sp.scRNAseqAnalysis"))
#remove .htseq suffix
colnames(counts) <- str_replace(colnames(counts), "(.*)\\.htseq$", "\\1")
colnames(counts.ercc) <- str_replace(colnames(counts.ercc), "(.*)\\.htseq$", "\\1")
#Select Singlets
s <- grepl("SRR", colnames(counts)) | grepl("Singlet", colnames(counts)) | grepl("NJA00102", colnames(counts)) | grepl("NJA00103", colnames(counts)) | grepl("NJA00104", colnames(counts)) | grepl("NJA00109", colnames(counts)) | grepl("NJA00204", colnames(counts)) | grepl("NJA00205", colnames(counts)) | grepl("NJA00206", colnames(counts))
#Create Objects with multiplets and Singlets
cObjSng <- spCounts(counts[, s], counts.ercc[, s])
cObjMul <- spCounts(counts[, !s], counts.ercc[, !s])
#Plot Fraction of ERCC in Multiplets and Singlets (Works poorly due to no ERCC in Regev data)
plotCountsERCC(cObjSng, cObjMul)
## Warning in estimateCells(spCountsSng, spCountsMul): These samples ERCC
## reads are all 0's: SRR5103562.A01, SRR5102813.A01, SRR5102362.A01,
## SRR5102747.A01, SRR5103063.A01, SRR5102513.A01, SRR5102923.A01,
## SRR5103085.A01, SRR5103186.A01, SRR5103184.A01, SRR5103110.A01,
## SRR5103393.A01, SRR5103426.A01, SRR5103175.A01, SRR5103846.A01,
## SRR5102378.A01, SRR5102729.A01, SRR5102951.A01, SRR5102761.A01,
## SRR5102728.A01, SRR5102073.A01, SRR5103743.A01, SRR5103309.A01,
## SRR5103561.A01, SRR5102842.A01, SRR5102752.A01, SRR5102876.A01,
## SRR5102868.A01, SRR5102664.A01, SRR5103035.A01, SRR5103131.A01,
## SRR5102565.A01, SRR5103000.A01, SRR5103367.A01, SRR5103137.A01,
## SRR5103336.A01, SRR5103672.A01, SRR5103695.A01, SRR5103355.A01,
## SRR5102991.A01, SRR5102624.A01, SRR5102617.A01, SRR5103260.A01,
## SRR5102917.A01, SRR5102662.A01, SRR5103453.A01, SRR5103182.A01,
## SRR5103334.A01, SRR5103836.A01, SRR5103019.A01, SRR5102611.A01,
## SRR5102861.A01, SRR5103277.A01, SRR5102934.A01, SRR5101983.A01,
## SRR5103056.A01, SRR5103267.A01, SRR5102380.A01, SRR5103368.A01,
## SRR5103150.A01, SRR5103307.A01, SRR5103540.A01, SRR5102502.A01,
## SRR5103148.A01, SRR5102987.A01, SRR5102434.A01, SRR5102356.A01,
## SRR5102606.A01, SRR5103557.A01, SRR5103130.A01, SRR5102521.A01,
## SRR5103758.A01, SRR5103295.A01, SRR5103630.A01, SRR5103720.A01,
## SRR5102541.A01, SRR5103305.A01, SRR5102014.A01, SRR5103486.A01,
## SRR5102141.A01, SRR5102818.A01, SRR5102687.A01, SRR5103413.A01,
## SRR5102570.A01, SRR5102633.A01, SRR5102503.A01, SRR5102548.A01,
## SRR5102538.A01, SRR5103237.A01, SRR5102888.A01, SRR5102735.A01,
## SRR5102439.A01, SRR5102833.A01, SRR5102556.A01, SRR5102514.A01,
## SRR5103014.A01, SRR5102056.A01, SRR5102912.A01, SRR5103489.A01,
## SRR5103384.A01, SRR5103405.A01, SRR5102978.A01, SRR5102441.A01,
## SRR5102599.A01, SRR5102781.A01, SRR5103126.A01, SRR5102407.A01,
## SRR5103154.A01, SRR5102594.A01, SRR5103406.A01, SRR5102638.A01,
## SRR5103340.A01, SRR5103236.A01, SRR5103537.A01, SRR5103300.A01,
## SRR5103046.A01, SRR5102609.A01, SRR5102462.A01, SRR5103129.A01,
## SRR5102937.A01, SRR5102967.A01, SRR5102468.A01, SRR5102677.A01,
## SRR5102580.A01, SRR5102695.A01, SRR5102079.A01, SRR5102402.A01,
## SRR5102776.A01, SRR5102543.A01, SRR5102406.A01, SRR5102837.A01,
## SRR5102484.A01, SRR5103751.A01, SRR5103193.A01, SRR5102973.A01,
## SRR5102135.A01, SRR5103518.A01, SRR5102144.A01, SRR5102645.A01,
## SRR5102505.A01, SRR5103036.A01, SRR5103264.A01, SRR5102961.A01,
## SRR5102563.A01, SRR5102764.A01, SRR5103096.A01, SRR5102654.A01,
## SRR5102559.A01, SRR5103212.A01, SRR5103456.A01, SRR5102831.A01,
## SRR5102622.A01, SRR5103190.A01, SRR5102576.A01, SRR5103074.A01,
## SRR5102995.A01, SRR5103559.A01, SRR5102849.A01, SRR5103439.A01,
## SRR5102699.A01, SRR5103243.A01, SRR5102834.A01, SRR5103244.A01,
## SRR5103446.A01, SRR5103407.A01, SRR5103377.A01, SRR5102825.A01,
## SRR5102993.A01, SRR5103455.A01, SRR5103231.A01, SRR5102515.A01,
## SRR5103500.A01, SRR5103532.A01, SRR5102736.A01, SRR5103682.A01,
## SRR5102501.A01, SRR5102474.A01, SRR5103214.A01, SRR5102520.A01,
## SRR5102984.A01, SRR5102375.A01, SRR5103045.A01, SRR5102593.A01,
## SRR5102632.A01, SRR5102524.A01, SRR5102516.A01, SRR5102819.A01,
## SRR5103065.A01, SRR5102690.A01, SRR5102390.A01, SRR5103449.A01,
## SRR5103266.A01, SRR5103242.A01, SRR5102794.A01, SRR5103071.A01,
## SRR5102670.A01, SRR5103166.A01, SRR5102812.A01, SRR5103298.A01,
## SRR5103410.A01, SRR5102814.A01, SRR5102636.A01, SRR5102800.A01,
## SRR5102915.A01, SRR5103575.A01, SRR5102674.A01, SRR5103081.A01,
## SRR5102147.A01, SRR5102755.A01, SRR5103401.A01, SRR5102357.A01,
## SRR5102600.A01, SRR5102691.A01, SRR5103053.A01, SRR5103815.A01,
## SRR5103173.A01, SRR5102589.A01, SRR5103262.A01, SRR5103463.A01,
## SRR5102344.A01, SRR5103533.A01, SRR5103472.A01, SRR5102590.A01,
## SRR5103531.A01, SRR5102445.A01, SRR5102467.A01, SRR5103232.A01,
## SRR5103223.A01, SRR5102921.A01, SRR5102397.A01, SRR5103735.A01,
## SRR5102751.A01, SRR5102500.A01, SRR5102683.A01, SRR5102422.A01,
## SRR5102473.A01, SRR5102877.A01, SRR5102650.A01, SRR5102828.A01,
## SRR5102742.A01, SRR5102346.A01, SRR5102082.A01, SRR5102363.A01,
## SRR5102028.A01, SRR5103278.A01, SRR5103438.A01, SRR5101959.A01,
## SRR5101984.A01, SRR5101971.A01, SRR5103428.A01, SRR5103658.A01,
## SRR5102631.A01, SRR5103834.A01, SRR5103066.A01, SRR5102911.A01,
## SRR5102682.A01, SRR5102525.A01, SRR5102411.A01, SRR5103114.A01,
## SRR5103167.A01, SRR5102592.A01, SRR5102132.A01, SRR5103191.A01,
## SRR5102561.A01, SRR5102673.A01, SRR5103030.A01, SRR5102768.A01,
## SRR5102864.A01, SRR5103076.A01, SRR5103125.A01, SRR5102564.A01,
## SRR5103136.A01, SRR5102557.A01, SRR5103122.A01, SRR5103008.A01,
## SRR5102431.A01, SRR5102420.A01, SRR5102795.A01, SRR5103169.A01,
## SRR5103170.A01, SRR5103149.A01, SRR5103700.A01, SRR5102546.A01,
## SRR5103424.A01, SRR5103158.A01, SRR5103088.A01, SRR5102161.A01,
## SRR5102477.A01, SRR5102542.A01, SRR5102360.A01, SRR5102097.A01,
## SRR5102899.A01, SRR5102613.A01, SRR5103804.A01, SRR5103090.A01,
## SRR5103224.A01, SRR5102450.A01, SRR5102022.A01, SRR5102165.A01,
## SRR5103679.A01, SRR5102933.A01, SRR5103680.A01, SRR5102095.A01,
## SRR5102063.A01, SRR5102739.A01, SRR5101992.A01, SRR5102948.A01,
## SRR5102409.A01, SRR5102449.A01, SRR5103115.A01, SRR5103265.A01,
## SRR5103333.A01, SRR5102044.A01, SRR5102151.A01, SRR5102785.A01,
## SRR5103551.A01, SRR5103422.A01, SRR5102618.A01, SRR5102863.A01,
## SRR5103699.A01, SRR5102466.A01, SRR5102579.A01, SRR5103283.A01,
## SRR5103397.A01, SRR5103352.A01, SRR5103187.A01, SRR5103545.A01,
## SRR5103859.A01, SRR5103319.A01, SRR5102807.A01, SRR5102684.A01,
## SRR5102458.A01, SRR5102457.A01, SRR5103327.A01, SRR5102994.A01,
## SRR5102555.A01, SRR5103178.A01, SRR5102118.A01, SRR5103068.A01,
## SRR5103628.A01, SRR5102765.A01, SRR5102726.A01, SRR5103842.A01,
## SRR5103199.A01, SRR5103681.A01, SRR5103457.A01, SRR5103809.A01,
## SRR5103423.A01, SRR5102845.A01, SRR5103073.A01, SRR5102442.A01,
## SRR5102552.A01, SRR5103323.A01, SRR5103443.A01, SRR5103385.A01,
## SRR5102610.A01, SRR5103753.A01, SRR5102998.A01, SRR5102603.A01,
## SRR5103257.A01, SRR5102708.A01, SRR5102981.A01, SRR5102518.A01,
## SRR5103254.A01, SRR5103302.A01, SRR5102945.A01, SRR5101961.A01,
## SRR5102504.A01, SRR5103399.A01, SRR5103195.A01, SRR5102796.A01,
## SRR5103306.A01, SRR5102037.A01, SRR5103642.A01, SRR5103764.A01,
## SRR5103001.A01, SRR5103805.A01, SRR5102145.A01, SRR5102087.A01,
## SRR5103830.A01, SRR5102456.A01, SRR5103357.A01, SRR5103041.A01,
## SRR5102806.A01, SRR5102359.A01, SRR5102887.A01, SRR5102530.A01,
## SRR5103337.A01, SRR5102577.A01, SRR5103354.A01, SRR5102149.A01,
## SRR5102608.A01, SRR5103209.A01, SRR5103365.A01, SRR5103498.A01,
## SRR5103145.A01, SRR5102068.A01, SRR5103495.A01, SRR5103318.A01,
## SRR5103715.A01, SRR5102770.A01, SRR5102389.A01, SRR5103058.A01,
## SRR5102730.A01, SRR5103142.A01, SRR5103374.A01, SRR5103554.A01,
## SRR5103202.A01, SRR5102985.A01, SRR5103797.A01, SRR5102382.A01,
## SRR5102649.A01, SRR5103049.A01, SRR5103383.A01, SRR5102582.A01,
## SRR5103587.A01, SRR5102808.A01, SRR5103341.A01, SRR5102598.A01,
## SRR5102722.A01, SRR5102990.A01, SRR5102658.A01, SRR5102982.A01,
## SRR5103322.A01, SRR5102342.A01, SRR5103080.A01, SRR5102583.A01,
## SRR5103370.A01, SRR5103294.A01, SRR5102574.A01, SRR5103116.A01,
## SRR5102713.A01, SRR5102989.A01, SRR5103263.A01, SRR5103270.A01,
## SRR5102163.A01, SRR5102738.A01, SRR5102655.A01, SRR5103124.A01,
## SRR5103251.A01, SRR5102529.A01, SRR5103521.A01, SRR5102754.A01,
## SRR5102120.A01, SRR5103673.A01, SRR5103176.A01, SRR5102783.A01,
## SRR5103563.A01, SRR5103507.A01, SRR5101998.A01, SRR5102347.A01,
## SRR5103010.A01, SRR5103510.A01, SRR5103487.A01, SRR5103331.A01,
## SRR5103752.A01, SRR5103359.A01, SRR5102492.A01, SRR5103430.A01,
## SRR5102689.A01, SRR5103198.A01, SRR5103311.A01, SRR5103087.A01,
## SRR5103255.A01, SRR5103015.A01, SRR5102660.A01, SRR5102364.A01,
## SRR5103284.A01, SRR5103057.A01, SRR5103530.A01, SRR5103348.A01,
## SRR5103042.A01, SRR5102954.A01, SRR5103555.A01, SRR5102536.A01,
## SRR5103210.A01, SRR5102426.A01, SRR5103061.A01, SRR5102929.A01,
## SRR5103664.A01, SRR5102663.A01, SRR5103002.A01, SRR5103215.A01,
## SRR5102746.A01, SRR5102646.A01, SRR5102757.A01, SRR5102373.A01,
## SRR5102693.A01, SRR5103522.A01, SRR5102659.A01, SRR5103692.A01,
## SRR5103558.A01, SRR5102485.A01, SRR5103409.A01, SRR5103807.A01,
## SRR5103360.A01, SRR5102551.A01, SRR5103776.A01, SRR5102706.A01,
## SRR5102980.A01, SRR5102350.A01, SRR5103020.A01, SRR5103206.A01,
## SRR5103025.A01, SRR5102522.A01, SRR5102417.A01, SRR5102679.A01,
## SRR5103070.A01, SRR5103450.A01, SRR51027
## Warning in estimateCells(spCountsSng, spCountsMul): These samples ERCC
## reads are all 0's: SRR5103562.A01, SRR5102813.A01, SRR5102362.A01,
## SRR5102747.A01, SRR5103063.A01, SRR5102513.A01, SRR5102923.A01,
## SRR5103085.A01, SRR5103186.A01, SRR5103184.A01, SRR5103110.A01,
## SRR5103393.A01, SRR5103426.A01, SRR5103175.A01, SRR5103846.A01,
## SRR5102378.A01, SRR5102729.A01, SRR5102951.A01, SRR5102761.A01,
## SRR5102728.A01, SRR5102073.A01, SRR5103743.A01, SRR5103309.A01,
## SRR5103561.A01, SRR5102842.A01, SRR5102752.A01, SRR5102876.A01,
## SRR5102868.A01, SRR5102664.A01, SRR5103035.A01, SRR5103131.A01,
## SRR5102565.A01, SRR5103000.A01, SRR5103367.A01, SRR5103137.A01,
## SRR5103336.A01, SRR5103672.A01, SRR5103695.A01, SRR5103355.A01,
## SRR5102991.A01, SRR5102624.A01, SRR5102617.A01, SRR5103260.A01,
## SRR5102917.A01, SRR5102662.A01, SRR5103453.A01, SRR5103182.A01,
## SRR5103334.A01, SRR5103836.A01, SRR5103019.A01, SRR5102611.A01,
## SRR5102861.A01, SRR5103277.A01, SRR5102934.A01, SRR5101983.A01,
## SRR5103056.A01, SRR5103267.A01, SRR5102380.A01, SRR5103368.A01,
## SRR5103150.A01, SRR5103307.A01, SRR5103540.A01, SRR5102502.A01,
## SRR5103148.A01, SRR5102987.A01, SRR5102434.A01, SRR5102356.A01,
## SRR5102606.A01, SRR5103557.A01, SRR5103130.A01, SRR5102521.A01,
## SRR5103758.A01, SRR5103295.A01, SRR5103630.A01, SRR5103720.A01,
## SRR5102541.A01, SRR5103305.A01, SRR5102014.A01, SRR5103486.A01,
## SRR5102141.A01, SRR5102818.A01, SRR5102687.A01, SRR5103413.A01,
## SRR5102570.A01, SRR5102633.A01, SRR5102503.A01, SRR5102548.A01,
## SRR5102538.A01, SRR5103237.A01, SRR5102888.A01, SRR5102735.A01,
## SRR5102439.A01, SRR5102833.A01, SRR5102556.A01, SRR5102514.A01,
## SRR5103014.A01, SRR5102056.A01, SRR5102912.A01, SRR5103489.A01,
## SRR5103384.A01, SRR5103405.A01, SRR5102978.A01, SRR5102441.A01,
## SRR5102599.A01, SRR5102781.A01, SRR5103126.A01, SRR5102407.A01,
## SRR5103154.A01, SRR5102594.A01, SRR5103406.A01, SRR5102638.A01,
## SRR5103340.A01, SRR5103236.A01, SRR5103537.A01, SRR5103300.A01,
## SRR5103046.A01, SRR5102609.A01, SRR5102462.A01, SRR5103129.A01,
## SRR5102937.A01, SRR5102967.A01, SRR5102468.A01, SRR5102677.A01,
## SRR5102580.A01, SRR5102695.A01, SRR5102079.A01, SRR5102402.A01,
## SRR5102776.A01, SRR5102543.A01, SRR5102406.A01, SRR5102837.A01,
## SRR5102484.A01, SRR5103751.A01, SRR5103193.A01, SRR5102973.A01,
## SRR5102135.A01, SRR5103518.A01, SRR5102144.A01, SRR5102645.A01,
## SRR5102505.A01, SRR5103036.A01, SRR5103264.A01, SRR5102961.A01,
## SRR5102563.A01, SRR5102764.A01, SRR5103096.A01, SRR5102654.A01,
## SRR5102559.A01, SRR5103212.A01, SRR5103456.A01, SRR5102831.A01,
## SRR5102622.A01, SRR5103190.A01, SRR5102576.A01, SRR5103074.A01,
## SRR5102995.A01, SRR5103559.A01, SRR5102849.A01, SRR5103439.A01,
## SRR5102699.A01, SRR5103243.A01, SRR5102834.A01, SRR5103244.A01,
## SRR5103446.A01, SRR5103407.A01, SRR5103377.A01, SRR5102825.A01,
## SRR5102993.A01, SRR5103455.A01, SRR5103231.A01, SRR5102515.A01,
## SRR5103500.A01, SRR5103532.A01, SRR5102736.A01, SRR5103682.A01,
## SRR5102501.A01, SRR5102474.A01, SRR5103214.A01, SRR5102520.A01,
## SRR5102984.A01, SRR5102375.A01, SRR5103045.A01, SRR5102593.A01,
## SRR5102632.A01, SRR5102524.A01, SRR5102516.A01, SRR5102819.A01,
## SRR5103065.A01, SRR5102690.A01, SRR5102390.A01, SRR5103449.A01,
## SRR5103266.A01, SRR5103242.A01, SRR5102794.A01, SRR5103071.A01,
## SRR5102670.A01, SRR5103166.A01, SRR5102812.A01, SRR5103298.A01,
## SRR5103410.A01, SRR5102814.A01, SRR5102636.A01, SRR5102800.A01,
## SRR5102915.A01, SRR5103575.A01, SRR5102674.A01, SRR5103081.A01,
## SRR5102147.A01, SRR5102755.A01, SRR5103401.A01, SRR5102357.A01,
## SRR5102600.A01, SRR5102691.A01, SRR5103053.A01, SRR5103815.A01,
## SRR5103173.A01, SRR5102589.A01, SRR5103262.A01, SRR5103463.A01,
## SRR5102344.A01, SRR5103533.A01, SRR5103472.A01, SRR5102590.A01,
## SRR5103531.A01, SRR5102445.A01, SRR5102467.A01, SRR5103232.A01,
## SRR5103223.A01, SRR5102921.A01, SRR5102397.A01, SRR5103735.A01,
## SRR5102751.A01, SRR5102500.A01, SRR5102683.A01, SRR5102422.A01,
## SRR5102473.A01, SRR5102877.A01, SRR5102650.A01, SRR5102828.A01,
## SRR5102742.A01, SRR5102346.A01, SRR5102082.A01, SRR5102363.A01,
## SRR5102028.A01, SRR5103278.A01, SRR5103438.A01, SRR5101959.A01,
## SRR5101984.A01, SRR5101971.A01, SRR5103428.A01, SRR5103658.A01,
## SRR5102631.A01, SRR5103834.A01, SRR5103066.A01, SRR5102911.A01,
## SRR5102682.A01, SRR5102525.A01, SRR5102411.A01, SRR5103114.A01,
## SRR5103167.A01, SRR5102592.A01, SRR5102132.A01, SRR5103191.A01,
## SRR5102561.A01, SRR5102673.A01, SRR5103030.A01, SRR5102768.A01,
## SRR5102864.A01, SRR5103076.A01, SRR5103125.A01, SRR5102564.A01,
## SRR5103136.A01, SRR5102557.A01, SRR5103122.A01, SRR5103008.A01,
## SRR5102431.A01, SRR5102420.A01, SRR5102795.A01, SRR5103169.A01,
## SRR5103170.A01, SRR5103149.A01, SRR5103700.A01, SRR5102546.A01,
## SRR5103424.A01, SRR5103158.A01, SRR5103088.A01, SRR5102161.A01,
## SRR5102477.A01, SRR5102542.A01, SRR5102360.A01, SRR5102097.A01,
## SRR5102899.A01, SRR5102613.A01, SRR5103804.A01, SRR5103090.A01,
## SRR5103224.A01, SRR5102450.A01, SRR5102022.A01, SRR5102165.A01,
## SRR5103679.A01, SRR5102933.A01, SRR5103680.A01, SRR5102095.A01,
## SRR5102063.A01, SRR5102739.A01, SRR5101992.A01, SRR5102948.A01,
## SRR5102409.A01, SRR5102449.A01, SRR5103115.A01, SRR5103265.A01,
## SRR5103333.A01, SRR5102044.A01, SRR5102151.A01, SRR5102785.A01,
## SRR5103551.A01, SRR5103422.A01, SRR5102618.A01, SRR5102863.A01,
## SRR5103699.A01, SRR5102466.A01, SRR5102579.A01, SRR5103283.A01,
## SRR5103397.A01, SRR5103352.A01, SRR5103187.A01, SRR5103545.A01,
## SRR5103859.A01, SRR5103319.A01, SRR5102807.A01, SRR5102684.A01,
## SRR5102458.A01, SRR5102457.A01, SRR5103327.A01, SRR5102994.A01,
## SRR5102555.A01, SRR5103178.A01, SRR5102118.A01, SRR5103068.A01,
## SRR5103628.A01, SRR5102765.A01, SRR5102726.A01, SRR5103842.A01,
## SRR5103199.A01, SRR5103681.A01, SRR5103457.A01, SRR5103809.A01,
## SRR5103423.A01, SRR5102845.A01, SRR5103073.A01, SRR5102442.A01,
## SRR5102552.A01, SRR5103323.A01, SRR5103443.A01, SRR5103385.A01,
## SRR5102610.A01, SRR5103753.A01, SRR5102998.A01, SRR5102603.A01,
## SRR5103257.A01, SRR5102708.A01, SRR5102981.A01, SRR5102518.A01,
## SRR5103254.A01, SRR5103302.A01, SRR5102945.A01, SRR5101961.A01,
## SRR5102504.A01, SRR5103399.A01, SRR5103195.A01, SRR5102796.A01,
## SRR5103306.A01, SRR5102037.A01, SRR5103642.A01, SRR5103764.A01,
## SRR5103001.A01, SRR5103805.A01, SRR5102145.A01, SRR5102087.A01,
## SRR5103830.A01, SRR5102456.A01, SRR5103357.A01, SRR5103041.A01,
## SRR5102806.A01, SRR5102359.A01, SRR5102887.A01, SRR5102530.A01,
## SRR5103337.A01, SRR5102577.A01, SRR5103354.A01, SRR5102149.A01,
## SRR5102608.A01, SRR5103209.A01, SRR5103365.A01, SRR5103498.A01,
## SRR5103145.A01, SRR5102068.A01, SRR5103495.A01, SRR5103318.A01,
## SRR5103715.A01, SRR5102770.A01, SRR5102389.A01, SRR5103058.A01,
## SRR5102730.A01, SRR5103142.A01, SRR5103374.A01, SRR5103554.A01,
## SRR5103202.A01, SRR5102985.A01, SRR5103797.A01, SRR5102382.A01,
## SRR5102649.A01, SRR5103049.A01, SRR5103383.A01, SRR5102582.A01,
## SRR5103587.A01, SRR5102808.A01, SRR5103341.A01, SRR5102598.A01,
## SRR5102722.A01, SRR5102990.A01, SRR5102658.A01, SRR5102982.A01,
## SRR5103322.A01, SRR5102342.A01, SRR5103080.A01, SRR5102583.A01,
## SRR5103370.A01, SRR5103294.A01, SRR5102574.A01, SRR5103116.A01,
## SRR5102713.A01, SRR5102989.A01, SRR5103263.A01, SRR5103270.A01,
## SRR5102163.A01, SRR5102738.A01, SRR5102655.A01, SRR5103124.A01,
## SRR5103251.A01, SRR5102529.A01, SRR5103521.A01, SRR5102754.A01,
## SRR5102120.A01, SRR5103673.A01, SRR5103176.A01, SRR5102783.A01,
## SRR5103563.A01, SRR5103507.A01, SRR5101998.A01, SRR5102347.A01,
## SRR5103010.A01, SRR5103510.A01, SRR5103487.A01, SRR5103331.A01,
## SRR5103752.A01, SRR5103359.A01, SRR5102492.A01, SRR5103430.A01,
## SRR5102689.A01, SRR5103198.A01, SRR5103311.A01, SRR5103087.A01,
## SRR5103255.A01, SRR5103015.A01, SRR5102660.A01, SRR5102364.A01,
## SRR5103284.A01, SRR5103057.A01, SRR5103530.A01, SRR5103348.A01,
## SRR5103042.A01, SRR5102954.A01, SRR5103555.A01, SRR5102536.A01,
## SRR5103210.A01, SRR5102426.A01, SRR5103061.A01, SRR5102929.A01,
## SRR5103664.A01, SRR5102663.A01, SRR5103002.A01, SRR5103215.A01,
## SRR5102746.A01, SRR5102646.A01, SRR5102757.A01, SRR5102373.A01,
## SRR5102693.A01, SRR5103522.A01, SRR5102659.A01, SRR5103692.A01,
## SRR5103558.A01, SRR5102485.A01, SRR5103409.A01, SRR5103807.A01,
## SRR5103360.A01, SRR5102551.A01, SRR5103776.A01, SRR5102706.A01,
## SRR5102980.A01, SRR5102350.A01, SRR5103020.A01, SRR5103206.A01,
## SRR5103025.A01, SRR5102522.A01, SRR5102417.A01, SRR5102679.A01,
## SRR5103070.A01, SRR5103450.A01, SRR51027
## Warning: Removed 1261 rows containing missing values (geom_point).
#I fixed this now in devel version 0.0.1.5. Samples that have no ERCC reads should have them set to NA instead of 0. Setting them to NA will give a warning when building the spCounts objects but that is ok.
#counts.ercc[, grepl("SRR", colnames(counts.ercc))] <- NA
#cObjSng <- spCounts(counts[, s], counts.ercc[, s])
#cObjMul <- spCounts(counts[, !s], counts.ercc[, !s])
#plotCountsERCC(cObjSng, cObjMul)
# Plot Number of Cells expressing both of selected markers
plotCountsMarkers(cObjSng, cObjMul, markers = c("Alpi", "Reg4"))
## Warning in estimateCells(spCountsSng, spCountsMul): These samples ERCC
## reads are all 0's: SRR5103562.A01, SRR5102813.A01, SRR5102362.A01,
## SRR5102747.A01, SRR5103063.A01, SRR5102513.A01, SRR5102923.A01,
## SRR5103085.A01, SRR5103186.A01, SRR5103184.A01, SRR5103110.A01,
## SRR5103393.A01, SRR5103426.A01, SRR5103175.A01, SRR5103846.A01,
## SRR5102378.A01, SRR5102729.A01, SRR5102951.A01, SRR5102761.A01,
## SRR5102728.A01, SRR5102073.A01, SRR5103743.A01, SRR5103309.A01,
## SRR5103561.A01, SRR5102842.A01, SRR5102752.A01, SRR5102876.A01,
## SRR5102868.A01, SRR5102664.A01, SRR5103035.A01, SRR5103131.A01,
## SRR5102565.A01, SRR5103000.A01, SRR5103367.A01, SRR5103137.A01,
## SRR5103336.A01, SRR5103672.A01, SRR5103695.A01, SRR5103355.A01,
## SRR5102991.A01, SRR5102624.A01, SRR5102617.A01, SRR5103260.A01,
## SRR5102917.A01, SRR5102662.A01, SRR5103453.A01, SRR5103182.A01,
## SRR5103334.A01, SRR5103836.A01, SRR5103019.A01, SRR5102611.A01,
## SRR5102861.A01, SRR5103277.A01, SRR5102934.A01, SRR5101983.A01,
## SRR5103056.A01, SRR5103267.A01, SRR5102380.A01, SRR5103368.A01,
## SRR5103150.A01, SRR5103307.A01, SRR5103540.A01, SRR5102502.A01,
## SRR5103148.A01, SRR5102987.A01, SRR5102434.A01, SRR5102356.A01,
## SRR5102606.A01, SRR5103557.A01, SRR5103130.A01, SRR5102521.A01,
## SRR5103758.A01, SRR5103295.A01, SRR5103630.A01, SRR5103720.A01,
## SRR5102541.A01, SRR5103305.A01, SRR5102014.A01, SRR5103486.A01,
## SRR5102141.A01, SRR5102818.A01, SRR5102687.A01, SRR5103413.A01,
## SRR5102570.A01, SRR5102633.A01, SRR5102503.A01, SRR5102548.A01,
## SRR5102538.A01, SRR5103237.A01, SRR5102888.A01, SRR5102735.A01,
## SRR5102439.A01, SRR5102833.A01, SRR5102556.A01, SRR5102514.A01,
## SRR5103014.A01, SRR5102056.A01, SRR5102912.A01, SRR5103489.A01,
## SRR5103384.A01, SRR5103405.A01, SRR5102978.A01, SRR5102441.A01,
## SRR5102599.A01, SRR5102781.A01, SRR5103126.A01, SRR5102407.A01,
## SRR5103154.A01, SRR5102594.A01, SRR5103406.A01, SRR5102638.A01,
## SRR5103340.A01, SRR5103236.A01, SRR5103537.A01, SRR5103300.A01,
## SRR5103046.A01, SRR5102609.A01, SRR5102462.A01, SRR5103129.A01,
## SRR5102937.A01, SRR5102967.A01, SRR5102468.A01, SRR5102677.A01,
## SRR5102580.A01, SRR5102695.A01, SRR5102079.A01, SRR5102402.A01,
## SRR5102776.A01, SRR5102543.A01, SRR5102406.A01, SRR5102837.A01,
## SRR5102484.A01, SRR5103751.A01, SRR5103193.A01, SRR5102973.A01,
## SRR5102135.A01, SRR5103518.A01, SRR5102144.A01, SRR5102645.A01,
## SRR5102505.A01, SRR5103036.A01, SRR5103264.A01, SRR5102961.A01,
## SRR5102563.A01, SRR5102764.A01, SRR5103096.A01, SRR5102654.A01,
## SRR5102559.A01, SRR5103212.A01, SRR5103456.A01, SRR5102831.A01,
## SRR5102622.A01, SRR5103190.A01, SRR5102576.A01, SRR5103074.A01,
## SRR5102995.A01, SRR5103559.A01, SRR5102849.A01, SRR5103439.A01,
## SRR5102699.A01, SRR5103243.A01, SRR5102834.A01, SRR5103244.A01,
## SRR5103446.A01, SRR5103407.A01, SRR5103377.A01, SRR5102825.A01,
## SRR5102993.A01, SRR5103455.A01, SRR5103231.A01, SRR5102515.A01,
## SRR5103500.A01, SRR5103532.A01, SRR5102736.A01, SRR5103682.A01,
## SRR5102501.A01, SRR5102474.A01, SRR5103214.A01, SRR5102520.A01,
## SRR5102984.A01, SRR5102375.A01, SRR5103045.A01, SRR5102593.A01,
## SRR5102632.A01, SRR5102524.A01, SRR5102516.A01, SRR5102819.A01,
## SRR5103065.A01, SRR5102690.A01, SRR5102390.A01, SRR5103449.A01,
## SRR5103266.A01, SRR5103242.A01, SRR5102794.A01, SRR5103071.A01,
## SRR5102670.A01, SRR5103166.A01, SRR5102812.A01, SRR5103298.A01,
## SRR5103410.A01, SRR5102814.A01, SRR5102636.A01, SRR5102800.A01,
## SRR5102915.A01, SRR5103575.A01, SRR5102674.A01, SRR5103081.A01,
## SRR5102147.A01, SRR5102755.A01, SRR5103401.A01, SRR5102357.A01,
## SRR5102600.A01, SRR5102691.A01, SRR5103053.A01, SRR5103815.A01,
## SRR5103173.A01, SRR5102589.A01, SRR5103262.A01, SRR5103463.A01,
## SRR5102344.A01, SRR5103533.A01, SRR5103472.A01, SRR5102590.A01,
## SRR5103531.A01, SRR5102445.A01, SRR5102467.A01, SRR5103232.A01,
## SRR5103223.A01, SRR5102921.A01, SRR5102397.A01, SRR5103735.A01,
## SRR5102751.A01, SRR5102500.A01, SRR5102683.A01, SRR5102422.A01,
## SRR5102473.A01, SRR5102877.A01, SRR5102650.A01, SRR5102828.A01,
## SRR5102742.A01, SRR5102346.A01, SRR5102082.A01, SRR5102363.A01,
## SRR5102028.A01, SRR5103278.A01, SRR5103438.A01, SRR5101959.A01,
## SRR5101984.A01, SRR5101971.A01, SRR5103428.A01, SRR5103658.A01,
## SRR5102631.A01, SRR5103834.A01, SRR5103066.A01, SRR5102911.A01,
## SRR5102682.A01, SRR5102525.A01, SRR5102411.A01, SRR5103114.A01,
## SRR5103167.A01, SRR5102592.A01, SRR5102132.A01, SRR5103191.A01,
## SRR5102561.A01, SRR5102673.A01, SRR5103030.A01, SRR5102768.A01,
## SRR5102864.A01, SRR5103076.A01, SRR5103125.A01, SRR5102564.A01,
## SRR5103136.A01, SRR5102557.A01, SRR5103122.A01, SRR5103008.A01,
## SRR5102431.A01, SRR5102420.A01, SRR5102795.A01, SRR5103169.A01,
## SRR5103170.A01, SRR5103149.A01, SRR5103700.A01, SRR5102546.A01,
## SRR5103424.A01, SRR5103158.A01, SRR5103088.A01, SRR5102161.A01,
## SRR5102477.A01, SRR5102542.A01, SRR5102360.A01, SRR5102097.A01,
## SRR5102899.A01, SRR5102613.A01, SRR5103804.A01, SRR5103090.A01,
## SRR5103224.A01, SRR5102450.A01, SRR5102022.A01, SRR5102165.A01,
## SRR5103679.A01, SRR5102933.A01, SRR5103680.A01, SRR5102095.A01,
## SRR5102063.A01, SRR5102739.A01, SRR5101992.A01, SRR5102948.A01,
## SRR5102409.A01, SRR5102449.A01, SRR5103115.A01, SRR5103265.A01,
## SRR5103333.A01, SRR5102044.A01, SRR5102151.A01, SRR5102785.A01,
## SRR5103551.A01, SRR5103422.A01, SRR5102618.A01, SRR5102863.A01,
## SRR5103699.A01, SRR5102466.A01, SRR5102579.A01, SRR5103283.A01,
## SRR5103397.A01, SRR5103352.A01, SRR5103187.A01, SRR5103545.A01,
## SRR5103859.A01, SRR5103319.A01, SRR5102807.A01, SRR5102684.A01,
## SRR5102458.A01, SRR5102457.A01, SRR5103327.A01, SRR5102994.A01,
## SRR5102555.A01, SRR5103178.A01, SRR5102118.A01, SRR5103068.A01,
## SRR5103628.A01, SRR5102765.A01, SRR5102726.A01, SRR5103842.A01,
## SRR5103199.A01, SRR5103681.A01, SRR5103457.A01, SRR5103809.A01,
## SRR5103423.A01, SRR5102845.A01, SRR5103073.A01, SRR5102442.A01,
## SRR5102552.A01, SRR5103323.A01, SRR5103443.A01, SRR5103385.A01,
## SRR5102610.A01, SRR5103753.A01, SRR5102998.A01, SRR5102603.A01,
## SRR5103257.A01, SRR5102708.A01, SRR5102981.A01, SRR5102518.A01,
## SRR5103254.A01, SRR5103302.A01, SRR5102945.A01, SRR5101961.A01,
## SRR5102504.A01, SRR5103399.A01, SRR5103195.A01, SRR5102796.A01,
## SRR5103306.A01, SRR5102037.A01, SRR5103642.A01, SRR5103764.A01,
## SRR5103001.A01, SRR5103805.A01, SRR5102145.A01, SRR5102087.A01,
## SRR5103830.A01, SRR5102456.A01, SRR5103357.A01, SRR5103041.A01,
## SRR5102806.A01, SRR5102359.A01, SRR5102887.A01, SRR5102530.A01,
## SRR5103337.A01, SRR5102577.A01, SRR5103354.A01, SRR5102149.A01,
## SRR5102608.A01, SRR5103209.A01, SRR5103365.A01, SRR5103498.A01,
## SRR5103145.A01, SRR5102068.A01, SRR5103495.A01, SRR5103318.A01,
## SRR5103715.A01, SRR5102770.A01, SRR5102389.A01, SRR5103058.A01,
## SRR5102730.A01, SRR5103142.A01, SRR5103374.A01, SRR5103554.A01,
## SRR5103202.A01, SRR5102985.A01, SRR5103797.A01, SRR5102382.A01,
## SRR5102649.A01, SRR5103049.A01, SRR5103383.A01, SRR5102582.A01,
## SRR5103587.A01, SRR5102808.A01, SRR5103341.A01, SRR5102598.A01,
## SRR5102722.A01, SRR5102990.A01, SRR5102658.A01, SRR5102982.A01,
## SRR5103322.A01, SRR5102342.A01, SRR5103080.A01, SRR5102583.A01,
## SRR5103370.A01, SRR5103294.A01, SRR5102574.A01, SRR5103116.A01,
## SRR5102713.A01, SRR5102989.A01, SRR5103263.A01, SRR5103270.A01,
## SRR5102163.A01, SRR5102738.A01, SRR5102655.A01, SRR5103124.A01,
## SRR5103251.A01, SRR5102529.A01, SRR5103521.A01, SRR5102754.A01,
## SRR5102120.A01, SRR5103673.A01, SRR5103176.A01, SRR5102783.A01,
## SRR5103563.A01, SRR5103507.A01, SRR5101998.A01, SRR5102347.A01,
## SRR5103010.A01, SRR5103510.A01, SRR5103487.A01, SRR5103331.A01,
## SRR5103752.A01, SRR5103359.A01, SRR5102492.A01, SRR5103430.A01,
## SRR5102689.A01, SRR5103198.A01, SRR5103311.A01, SRR5103087.A01,
## SRR5103255.A01, SRR5103015.A01, SRR5102660.A01, SRR5102364.A01,
## SRR5103284.A01, SRR5103057.A01, SRR5103530.A01, SRR5103348.A01,
## SRR5103042.A01, SRR5102954.A01, SRR5103555.A01, SRR5102536.A01,
## SRR5103210.A01, SRR5102426.A01, SRR5103061.A01, SRR5102929.A01,
## SRR5103664.A01, SRR5102663.A01, SRR5103002.A01, SRR5103215.A01,
## SRR5102746.A01, SRR5102646.A01, SRR5102757.A01, SRR5102373.A01,
## SRR5102693.A01, SRR5103522.A01, SRR5102659.A01, SRR5103692.A01,
## SRR5103558.A01, SRR5102485.A01, SRR5103409.A01, SRR5103807.A01,
## SRR5103360.A01, SRR5102551.A01, SRR5103776.A01, SRR5102706.A01,
## SRR5102980.A01, SRR5102350.A01, SRR5103020.A01, SRR5103206.A01,
## SRR5103025.A01, SRR5102522.A01, SRR5102417.A01, SRR5102679.A01,
## SRR5103070.A01, SRR5103450.A01, SRR51027
#Create tSNE and plot with Mlcust clusters as well as gene expression
uObj <- spUnsupervised(cObjSng)
plotUnsupervisedClass(uObj, cObjSng)
#even though the seed is set by default I would: plotUnsupervisedClass(uObj, cObjSng, seed = 438923)
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Lgr5")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Olfm4")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Alpi")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Muc2")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Lyz1")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Reg4")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Ptprc")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Dclk1")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Mboat1")
plotUnsupervisedMarkers(uObj, cObjSng, markers = "Chga")
#Manually Create New Clusters by deducing cell types based on gene expression in clusters
classification <- getData(uObj, "classification")
names(classification) <- getData(uObj, "tsne") %>%
rownames()
SI.Stem <- names(classification)[classification %in% c("A1", "J1", "K1", "N1", "T1")]
SI.TA.Cells <- names(classification)[classification %in% c("R1", "C1", "B1")]
SI.Enterocyte.Progenitor <- names(classification)[classification %in% c("E1", "Q1")]
SI.Early.Enterocyte <- names(classification)[classification == "G1"]
SI.Late.Enterocyte <- names(classification)[classification == "M1"]
SI.Paneth <- names(classification)[classification %in% c("P1", "O1")]
SI.Goblet <- names(classification)[classification %in% c("F1", "L1")]
Blood.Cells <- names(classification)[classification == "D1"]
SI.Tuft.Cells <- names(classification)[classification == "H1"]
SI.Enteroendocrine <- names(classification)[classification == "S1"]
Colon <- names(classification)[classification == "I1"]
#tSNE for colon cells
cs <- colnames(counts) %in% Colon
#Colon object
colcObjSng <- spCounts(counts[, cs], counts.ercc[, cs])
#tSNE for Colon cell and expression of markers
C.uObj <- spUnsupervised(colcObjSng)
plotUnsupervisedClass(C.uObj, colcObjSng)
plotUnsupervisedMarkers(C.uObj, colcObjSng, markers = c("Lgr5"))
plotUnsupervisedMarkers(C.uObj, colcObjSng, markers = c("Muc2"))
plotUnsupervisedMarkers(C.uObj, colcObjSng, markers = c("Car1"))
#Select and rename clusters according to cell types in colon
C.classification <- getData(C.uObj, "classification")
names(C.classification) <- getData(C.uObj, "tsne") %>%
rownames()
C.Stem <- names(C.classification)[C.classification == "B1"]
C.Goblet <- names(C.classification)[C.classification == "C1"]
C.Colonocytes <- names(C.classification)[C.classification == "A1"]
#Organize new classifications and insert them into uObj which contains all cells
celltypes <- data.frame(
Samples = c(SI.Early.Enterocyte, SI.Enterocyte.Progenitor, SI.Enteroendocrine, SI.Goblet, SI.Late.Enterocyte, SI.Paneth, SI.Stem, SI.TA.Cells, C.Colonocytes, C.Goblet, C.Stem, SI.Tuft.Cells, Blood.Cells),
class = c(rep("SI.Early.Enterocyte", length(SI.Early.Enterocyte)), rep("SI.Enterocyte.Progenitor", length(SI.Enterocyte.Progenitor)), rep("SI.Enteroendocrine", length(SI.Enteroendocrine)), rep("SI.Goblet", length(SI.Goblet)), rep("SI.Late.Enterocyte", length(SI.Late.Enterocyte)), rep("SI.Paneth", length(SI.Paneth)), rep("SI.Stem", length(SI.Stem)), rep("SI.TA.Cells", length(SI.TA.Cells)), rep("C.Colonocytes", length(C.Colonocytes)), rep("C.Goblet", length(C.Goblet)), rep("C.Stem", length(C.Stem)), rep("SI.Tuft.Cells", length(SI.Tuft.Cells)), rep("Blood.Cells", length(Blood.Cells)))
)
newclass <- celltypes[match(rownames(getData(uObj, "tsne")), celltypes$Samples),]
newclass <- as.vector(newclass$class)
#devtools::use_data(newclass, overwrite = TRUE)
uObj@classification <- newclass
#Plot tsne with new clusters
plotUnsupervisedClass(uObj, cObjSng)
#Calculate new means for groups
tsneMeans(uObj) <- tsneGroupMeans(getData(uObj, "tsne"), getData(uObj, "classification"))
groupMeans(uObj) <- averageGroupExpression(cObjSng, getData(uObj, "classification"), weighted=FALSE)
#Set Uncertainty to 0 and attempt to identify cell composition of multiplets
uncertainty(uObj) <- rep(0, length(getData(uObj, "uncertainty")))
#sObj <- spSwarm(cObjMul, uObj, distFun = "dtsnCellNum", e = 0.0025, cellNumbers = estimateCells(cObjSng, cObjMul), swarmsize = 500, maxiter = 1000)
#plotSwarmGraph(sObj, uObj)
#Check false positives by seeing how many of multiplets contain cells from both SI and Colon
#fp <- getMultipletsForEdge(sObj, edges = data.frame(to = "C.Stem", from = "SI.Stem"), edge.cutoff = 0)
#fp
#devtools::use_data(sObj, overwrite = TRUE)
#devtools::use_data(fp, overwrite = TRUE)
#sObj <- spSwarm(cObjMul, uObj, distFun = "distToSliceNorm")
#plotSwarm(sObj, uObj, cObjSng, cObjMul, type = "tsne")
#plotSwarm(sObj, uObj, cObjSng, cObjMul, type = "heat")
#tsne <- getData(uObj, "tsne")
#plot.nice(tsne, gene.vals=counts.log, genes=c("Lyz1", "Alpi", "Lgr5", "Reg4", "Dll4"), cex=2)
sessionInfo()
## R version 3.4.3 (2017-11-30)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS High Sierra 10.13.3
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] bindrcpp_0.2 forcats_0.2.0 stringr_1.2.0
## [4] dplyr_0.7.4 purrr_0.2.4 readr_1.1.1
## [7] tidyr_0.8.0 tibble_1.4.2 ggplot2_2.2.1.9000
## [10] tidyverse_1.2.1 sp.scRNAseq_0.0.1.5
##
## loaded via a namespace (and not attached):
## [1] viridis_0.5.0 httr_1.3.1 tidygraph_1.1.0
## [4] jsonlite_1.5 viridisLite_0.3.0 ggraph_1.0.1
## [7] modelr_0.1.1 pso_1.0.3 assertthat_0.2.0
## [10] stats4_3.4.3 selectr_0.3-1 cellranger_1.1.0
## [13] progress_1.1.2.9002 yaml_2.1.16 ggrepel_0.7.0
## [16] pillar_1.1.0.9000 backports_1.1.2 lattice_0.20-35
## [19] glue_1.2.0 digest_0.6.15 rvest_0.3.2
## [22] colorspace_1.3-2 htmltools_0.3.6 plyr_1.8.4
## [25] psych_1.7.8 XML_3.98-1.9 pkgconfig_2.0.1
## [28] broom_0.4.3 haven_1.1.1 scales_0.5.0.9000
## [31] tweenr_0.1.5 Rtsne_0.13 ggforce_0.1.1
## [34] withr_2.1.1.9000 ansistrings_1.0.0.9000 BiocGenerics_0.24.0
## [37] lazyeval_0.2.1 cli_1.0.0.9001 mnormt_1.5-5
## [40] magrittr_1.5 crayon_1.3.4 readxl_1.0.0
## [43] mclust_5.4 evaluate_0.10.1 nlme_3.1-131
## [46] MASS_7.3-47 xml2_1.2.0 foreign_0.8-69
## [49] ggthemes_3.4.0 prettyunits_1.0.2 tools_3.4.3
## [52] hms_0.4.1 rgeolocate_1.0.1 S4Vectors_0.16.0
## [55] munsell_0.4.3 compiler_3.4.3 rlang_0.2.0.9000
## [58] units_0.5-1 grid_3.4.3 rstudioapi_0.7
## [61] igraph_1.1.2 labeling_0.3 rmarkdown_1.9
## [64] gtable_0.2.0 curl_3.1 rematch2_2.0.1
## [67] reshape2_1.4.3 R6_2.2.2 gridExtra_2.3
## [70] lubridate_1.7.1 knitr_1.19 udunits2_0.13
## [73] bindr_0.1 rprojroot_1.3-2 stringi_1.1.6
## [76] parallel_3.4.3 Rcpp_0.12.15